Abstract

From Jan. 1, 2009, to May 31, 2013, 15, 287 respiratory specimens submitted to the Clinical Virology laboratory at Children’s Hospital Colorado were tested for human coronavirus RNA by RT-PCR. Human coronaviruses HKU1, OC43, 229E, and NL63 co-circulated during each of the respiratory seasons but with significant year to year variability, and cumulatively accounted for 7.4 - 15.6% of all samples tested during months of peak activity. A total of 79 (0.5% prevalence) specimens were positive for human betacoronavirus HKU1 RNA. Genotypes HKU1 A and B were both isolated from clinical specimens and propagated on primary human tracheal-bronchial epithelial cells cultured at the air-liquid interface and were neutralized in vitro by human intravenous immunoglobulin and by polyclonal rabbit antibodies to the spike glycoprotein of HKU1. Phylogenetic analysis of deduced amino acid sequences of 7 full length genomes of Colorado HKU1 viruses and the spike glycoproteins from 4 additional HKU1 viruses from Colorado and 3 from Brazil, demonstrated remarkable conservation of these sequences with genotypes circulating in Hong Kong and France. Within genotype A, all but one of the Colorado HKU1 sequences formed a unique subclade defined by 3 amino acid residue substitutions (W197F, F613Y, S752F) in the spike glycoprotein and exhibited a unique signature in the acidic tandem repeat in the N terminal region of the nsp3 subdomain. Elucidating the function of and mechanisms responsible for the formation of theses varying tandem will increase our understanding of the replication process and pathogenicity of HKU1 and potentially other coronaviruses.